----- Original Message ----- > From: "Tom Harrop" <twharr...@gmail.com> > Cc: "bioc-devel" <bioc-devel@r-project.org>, "Bioconductor mailing list" > <bioconduc...@r-project.org> > Sent: Tuesday, May 6, 2014 1:25:57 AM > Subject: Re: [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages > available for BioC 2.14 > > Hi Dan, > > Thanks a lot for the update. > > I can’t get DESeq2 to load after installing it on my Mavericks build. > > biocLite(‘DESeq2’) runs without error, but library(‘DESeq2’) returns > the > error: > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > versionCheck > > = vI[[j]]) : > > there is no package called ‘annotate’ > > Error: package or namespace load failed for ‘DESeq2’ > > biocLite(‘annotate’) or install.packages(‘annotate’) both return: > > > Warning message: > > package ‘annotate’ is not available (for R version 3.1.0) > > I’ve tried a couple of different CRAN mirrors without luck. Is > annotate one > of the packages that still needs to be updated for Mavericks? >
Yes, you can tell by going to the annotate landing page (http://www.bioconductor.org/packages/2.14/bioc/html/annotate.html) and seeing whether a Mavericks package is listed under Package Downloads at the bottom. I don't think there's a problem with the code in the package; rather, it has issues because its examples try to contact flaky web services. I'll see if we can do something to make this package available. Thanks, Dan > Thanks, > > Tom > > > sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-apple-darwin13.1.0 (64-bit) > > locale: > > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets > > methods > > [8] base > > other attached packages: > > [1] RcppArmadillo_0.4.200.0 Rcpp_0.11.1 > > GenomicRanges_1.16.3 > > [4] GenomeInfoDb_1.0.2 IRanges_1.22.6 > > BiocGenerics_0.10.0 > > [7] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > > [1] Biobase_2.24.0 RColorBrewer_1.0-5 stats4_3.1.0 > > tools_3.1.0 > > > > [5] XVector_0.4.0 > > > > On 6 May 2014 00:37, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > > > Hi all, > > > > Bioconductor 2.14 (release) packages are now available for the > > Mavericks > > (Mac OS X 10.9) build of R. > > > > If you install this version of R, you can install Mavericks > > packages by > > typing: > > > > source("http://bioconductor.org/biocLite.R") > > > > ...and then using biocLite() to install the package(s) you want; > > for > > example: > > > > biocLite("BiocGenerics") > > > > There are still a few packages that aren't building on Mavericks. > > We have > > been in touch > > with their maintainers in most cases and hope that they'll be > > building > > soon. If you are > > the maintainer of one of these packages, feel free to contact us on > > bioc-devel if you > > need help getting your package to build. > > Most of the issues have to do with the fact that this version of R > > uses > > clang/clang++ > > instead of gcc/g++ to compile C/C++ code. > > > > If you need to use a package that's not yet available on Mavericks, > > you > > can continue > > to use the Snow Leopard build of R; it will work fine on Mavericks. > > > > Mavericks binaries for BioC-devel (3.0) will be available in the > > coming > > weeks. > > > > Dan > > > > _______________________________________________ > > Bioconductor mailing list > > bioconduc...@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > bioconduc...@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel